ClearVolume
is an open source real-time live
3D visualization library designed for high-end volumetric
light sheet microscopes. ClearVolume enables the live visualization of microscope data - allowing the biologists to immediately decide whether a sample is worth imaging. ClearVolume can easily be integrated into existing
Java
Java is one of the Greater Sunda Islands in Indonesia. It is bordered by the Indian Ocean to the south and the Java Sea (a part of Pacific Ocean) to the north. With a population of 156.9 million people (including Madura) in mid 2024, proje ...
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C/C++
The C and C++ programming languages are closely related but have many significant differences. C++ began as a fork of an early, pre-standardized C, and was designed to be mostly source-and-link compatible with C compilers of the time. Due to ...
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Python
Python may refer to:
Snakes
* Pythonidae, a family of nonvenomous snakes found in Africa, Asia, and Australia
** ''Python'' (genus), a genus of Pythonidae found in Africa and Asia
* Python (mythology), a mythical serpent
Computing
* Python (prog ...
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LabVIEW based microscope software. It has a dedicated interface to MicroManager/OpenSpim/OpenSpin control software. ClearVolume supports multi-channels, live 3D data streaming from remote microscopes, and uses a multi-pass Fibonacci rendering algorithm that can handle large volumes. Moreover, ClearVolume is integrated into the
FiJi
Fiji, officially the Republic of Fiji, is an island country in Melanesia, part of Oceania in the South Pacific Ocean. It lies about north-northeast of New Zealand. Fiji consists of an archipelago of more than 330 islands—of which about ...
/
ImageJ2/
KNIME
KNIME (), the Konstanz Information Miner, is a data analytics, reporting and integrating platform. KNIME integrates various components for machine learning and data mining through its modular data pipelining "Building Blocks of Analytics" con ...
ecosystem.
See also
*
FiJi
Fiji, officially the Republic of Fiji, is an island country in Melanesia, part of Oceania in the South Pacific Ocean. It lies about north-northeast of New Zealand. Fiji consists of an archipelago of more than 330 islands—of which about ...
*
KNIME
KNIME (), the Konstanz Information Miner, is a data analytics, reporting and integrating platform. KNIME integrates various components for machine learning and data mining through its modular data pipelining "Building Blocks of Analytics" con ...
*
Light sheet fluorescence microscopy
Light sheet fluorescence microscopy (LSFM) is a fluorescence microscopy technique with an intermediate-to-high optical resolution, but good optical sectioning capabilities and high speed. In contrast to epifluorescence microscopy only a thin sl ...
*
Volume rendering
In scientific visualization and computer graphics, volume rendering is a set of techniques used to display a 2D projection of a 3D discretely sampled data set, typically a 3D scalar field.
A typical 3D data set is a group of 2D slice image ...
References
{{reflist, refs=
[
{{cite journal
, author1=Royer, Loïc A , author2=Weigert, Martin , author3=Günther, Ulrik , author4=Maghelli, Nicola , author5=Jug, Florian , author6=Sbalzarini, Ivo F. , author7=Myers, Eugene W. , title = ClearVolume – Open-source live 3D visualization for light sheet microscopy.
, journal = Nature Methods
, volume = 12
, issue=6 , date = 2015
, url = http://www.nature.com/nmeth/journal/v12/n6/full/nmeth.3372.html
, doi = 10.1038/nmeth.3372 , pages=480–481 , pmid=26020498, s2cid=205423715 , url-access=subscription
]
External links
Website of the open source ClearVolume project with links to the wiki, code repositories and issue tracking.
ClearVolume KNIME plugin project page.
ClearVolume FiJi plugin project page.
Computational science
Bioinformatics